About this Author

College chemistry, 1983

The 2002 Model

After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases.
To contact Derek email him directly: derekb.lowe@gmail.com
Twitter: Dereklowe

April 29, 2011

Keep On Scrollin'

Posted by Derek

I've been browsing through my journal RSS feeds, and a question occurs to me. When you're scanning through the current literature, what sort of paper makes you most likely to keep scrolling? What kind of work are you least likely to actually read?

We'll stipulate that you're looking at a journal or subject that's relevant to your field - I read a lot of stuff, but I'm most certainly not going to slow down to look over (say) a theoretical paper calculating the stability of isomeric inorganic complexes. But that said, there are things that make you slow down while going through the abstracts, and there are things that absolutely made you speed up.

My particular biases are to walk more quickly past the following sorts of titles, which have been only slightly exaggerated for effect. And you?

"Synthesis of A Natural Product That You Don't Care About, Using Methods That Bore You"

"Slight Enantiomeric Excess Realized Through Use Of A Humungous Catalyst That Takes Nine Steps To Make All By Itself"

"Nanorods Attached to Nanoplates by Nanosprings: Progress Toward a Nanomattress"

"Green Chemistry, Part 87: A Novel Reagent to Prepare Nitriles from Oximes"

"Isolation Of Known Terpenoid Natural Products From Weeds In Our Back Yard"

"Structure- and Fragment-Based Design, Traditional and Parallel Synthesis, and Evaluation of Novel, Really Big and Greasy, Fused Heterocycles Containing Substituents Easily Analoged By Our CRO Chemists Overseas as Potent Modulators of that Recent Really Exciting Protein Found by a Well Known Academic Lab and Published in Nature Which Left Out Critical Experimental Details So We Had to Develop Everything Ourselves, Towards the Potential, But Unlikely Really, Treatment of that Condition for which Our Company Can Charge a Lot of Money"

2. Anything involving cryo-electron microscopy -- sort of a Rorschack test allowing you to see what you want

3. Anything involving Aplysia, C. elegans or rodent models of learning -- way too far from humans to be relevant.

4. Anything with mathematical modeling of intercellular (or extracellular events). In most cases we simply don't know all the players -- this leaves out modeling in biophysics (e.g. Hodgkin Huxley etc. etc.).

5. Any detailed paper on protein folding (I just don't know enough to read it intelligently -- hopefully, this is the year of serious PChem and physical organic chemistry and then I'll be able to tackle this stuff and be able to read the sacred texts in the original).

I don't generally ignore them altogether, but I do take a deep breath before reading articles with titles that use a flashy new name for something that scientists have been doing for a very long time in order to make it sound new and sexy and worthy of being on the cover of Nature or Science or attracting VCs. In pursuit of sexiness, articles with such titles often bypass stodgy-old-fart things like controls or the fact that somebody else already did the same thing a long time ago. Specific phrases that come to mind right off are:

ANY paper that CLAIMS to describe probing/understanding molecular interactions using AFM. Really?? That certainly is a real nice Adobe graphic you've created that shows a bunch of neat (ordered) molecules on a surface and some sort of organically appended AFM tip bouncing up and down.
"we've interpreted this force curve to mean...." what exactly???

I always find the word 'novel' a turn off and if reviewing a manuscript I always suggest (sometimes insist) that to be removed. I just think that it sounds so silly and cringeworthy especially given some fo the crap that it gets applied to.

Here are my contributions (admittedly more exaggerated than Derek's set):

Novel, highly predictive proprietary QSAR models for hERG blockade, fully tested and validated, using data that you will never get to see.

New and Original strategies for Predictive Chemistry: Why use knowledge when fifty cross-correlated molecular descriptors and a consensus of over-fit models will tell you the same thing?

Good question Derek. I wasn't sure of the answer so I looked at the last two JACS just to see what I do. It appears that I pass over just about everything. I only stop if I recognize an author (where are they now?) or if there is a specific organic structure that catches my attention.

There was one paper that I looked at further where the author started with a simple 3-furanone and made complexmolecumycin. I remembered from 30+ years ago that 3-furanones are not so easy to come by and they go to crap easily so I followed the references and, sure enough, they're still a pain to come by.

And Rick is spot on with the renaming thing. It's annoying and we all know who the culprits are.

"I’ve been puzzling over this idea. How would a budding chemist do these “chemical free” experiments when everything in the box from plastic to paper is made of chemical compounds? One could imagine that these small scientists might put water in the plastic test tubes pictured below. But, no, that would be H2O. Another known chemical compound."

"The Activity of A Protein Abbreviated By A Long Alphanumeric Code That May Just As Easily Be The Serial Number from Your Washing Machine is Modulated Weakly by Another Long, Alphanumeric Protein That Promiscuously Binds To Everything Anyway"

@Derek: What RSS reader do you find useful for journals? I tried a few of the add-ons in Firefox and have been disappointed that they only feed the titles, and nothing from the abstracts. Or is that what I should expect?

j,
Your generosity of spirit is breathtaking. Indeed, I am profoundly moved that I breath the same air as you, let alone share overlapping blog-space. Somehow it helps me deal with the thought that I may never be like you. Please know that Serious People with Informed Opinions like you make a big difference every day in the lives of people like me, who group-think uninformed opinions and force them on you. Where would we be without you?!
Your humbled and obedient servant - Rick

I find some computational chemistry interesting, but most molecular dynamics papers make me scroll faster, as will papers about shooting lasers at things. The "New dye sensitized solar cell gets 6% efficiency and still uses ruthenium" paper is the bane of my existence. I can avoid it on the feed, but someone will present it in group meeting, and I'll be rolling my eyes the whole time. "New Suzuki coupling indistinguishable in all ways from old Suzuki coupling" paper is definitely a pass, as are most papers that have the initials "EE" anywhere on the page. "Rhodium catalyst puts together strange rings from acetylene and acrolein" paper is a guilty pleasure of mine, as are a lot of "concise total synthesis" papers. "Large polymer sack full of cisplatin" paper is another that I move away from as fast as possible.

Luysii, every single item on this list lends itself to good and bad examples. There are good examples of virtual screening, mathematical modeling, protein folding and MD. MD is generally a very slow technique and it's a stretch to use it for protein folding but it can be very useful for specific problems if used intelligently. As usual, no technique or approach is going to make you swoon if it's being used for solving the wrong problem.

I skip anything from China, India, Korea, most asian countries in fact as personal experience has proved to me that 9/10 procedures don't work and hence it's probably fabricated.
Yes, I know this is controversial but I also tend to flash past papers from Italy, France, Spain and most eastern europe sources, plus South American. I know a lot of reputable scientists in these countries and lot of good work comes out of these centres, but unfortunately so does a lot of unreproducible garbage.

Apologies for being late to party.
#26 Rick - You missed one:
"Explaining MBAs to Scientists" [without making them foam at mouth?]
When I have time, I scan med rel papers only, and skip anything with "aspirin for treating...." in the title ;-)
Its just so *yesterday's news*, know what I mean?

37 Anon -- why do molecular dynamics papers make you scroll ? Do you have a problem trusting the results? No axe to grind, just asking.

MD is highly technical, and I don't have a background. In some cases I've been able to extract useful information from time independant ab-initio stuff, as it jives with my physical organic and semiconductor background, but I usually have no idea what to do with MD. In some cases I've tried, but I haven't come away feeling better informed.